- Email: [email protected]
Karyotypically distinct U251, U373, and SNB19 glioma cell lines are of the same origin but have different drug treatment sensitivities
Gene 540 (2014) 263–265
Contents lists available at ScienceDirect
Gene journal homepage: www.elsevier.com/locate/gene
Letter to the Editor Karyotypically distinct U251, U373, and SNB19 glioma cell lines are of the same origin but have different drug treatment sensitivities Keywords: Glioblastoma Karyotype Drug resistance Chromosome instability Aneuploidy
Dear Editor, We have read Letter to the Editor entitled Identity confusion of glioma cell lines by Timerman and Yeung (2014) and share concern and great interest to U251 and U373 cell lines misidentity and their wide use in research community as unrelated glioma cell lines. Actually, mutation analysis (Fuxe et al., 2000 and Refs. herein) and short tandem repeatspolymerase chain reaction (STR-PCR) analysis (see Refs. in Timerman and Yeung, 2014) of U373 cell stocks from The American Type Culture Collection (ATCC) and The European Collection of Cell Cultures (ECACC) revealed that U373 cells were identical to and derived from U251 cells. The picture gets more complicated with the fact that mutation analysis of cancer genes in NCI-60 cell line panel led to a suggestion that SNB19 cell line was also related to U251 cell line (Ikediobi et al., 2006). The following STR-PCR analysis of U251 and SNB19 cells showed their high similarity (Lorenzi et al., 2009) and pair-wise comparisons of the genotype calls from the single nucleotide polymorphism (SNP) mapping arrays confirmed very high identity of U251, U373, and SNB19 cell lines (Demichelis et al., 2008; http://www.sanger.ac.uk/ genetics/CGP/Genotyping/nci60.shtml). Our analysis of literature data supports the observation made by Timerman and Yeung (2014) that U251 and U373 cells behaved similarly in many works. We add that SNB19 and U251/U373 cells also demonstrated similar behavior in diverse experiments (e.g., Li et al., 2008; Malla et al., 2011; Zhao et al., 2006). However, despite the high identity and consistent results in various metrics, differences in sensitivity to drugs are well documented for this cell line lineage. It was reported that in sharp contrast to U251 cells, U373 cells (both lines of
Abbreviations: ATCC, The American Type Culture Collection; CDKN2A, cyclindependent kinase inhibitor 2A; CIN, chromosome instability; CNV, copy number variation; ECACC, The European Collection of Cell Cultures; FDA, Food and Drug Administration; FLIPS, FLICE-like inhibitory protein short; LOH, loss of heterozygosity; NCI-60, The National Cancer Institute 60 human tumor cell line anticancer drug screen; PTEN, phosphatase and tensin homolog; STR-PCR, short tandem repeats-polymerase chain reaction; SNP, single nucleotide polymorphism; S6K1, ribosomal protein S6 kinase 1; TP53, tumor protein p53; TMZ, temozolomide; TRAIL, tumor necrosis factor-related apoptosisinducing ligand.
http://dx.doi.org/10.1016/j.gene.2014.02.053 0378-1119/© 2014 Elsevier B.V. All rights reserved.
unmentioned origin) were insensitive to treatment with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). Molecular analysis revealed that cell lines differed in translation of the FLICE-like inhibitory protein short (FLIPS) mRNAs, a key regulator of TRAIL sensitivity, due to different activities of ribosomal protein S6 kinase 1 (S6K1) arm of the PI3K–mTOR–AKT pathway (Panner et al., 2005). Another research group showed that combining flavonoid quercetin with TRAIL strongly augmented TRAIL-mediated apoptosis in U251 cells but U373 cells were completely resistant (both cell lines from ATCC). The difference in sensitivity was attributed to the fact that quercetin treatment suppressed protein expression of survinin, an inhibitor of apoptosis protein, only in U251 (Siegelin et al., 2009). The growth inhibition of U251 cells was significantly more profound after erlotinib treatment (epidermal growth factor receptor inhibitor) in comparison to U373 cells (both cell lines from Institut de Recerca Hospital Universitari Vall d'Hebron, Barcelona) (Ramis et al., 2012). However, comparable erlotinib sensitivity was shown for U251 and SNB19 cells (from NCI-60 cell line panel) (Abaan et al., 2013). MEK inhibitor alone significantly reduced cell growth and cyclin D1 levels in U373 but not U251 cells (both cell lines from the UCSF BTRC Tissue Core). Only combined treatment with MEK inhibitor and dual PI3K/mTOR inhibitor induced similar response in U251 cells (See et al., 2012). SNB19 cells were more resistant to 1-t-butyl carbamoyl, 7-methyl-indole-3-ethyl isothiocyanate (NB7M), paclitaxel, and dasatinib treatment than U251 cells (both cell lines from NCI-60 cell line panel) (Brard et al., 2009; Moghaddas Gholami et al., 2013). SNB19 (from German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany) and U373 cells were less sensitive to imatinib or sunitinib treatment than U251 (the letter two lines provided by Professor Joseph Costello). Phospho-receptor tyrosine kinase (pRTK) arrays showed the different effect of cediranib and sunitinib treatment on pRTKs in U251, U373, and SNB19 cells. Furthermore, SNB19 cells were more resistant to temozolomide treatment alone or combined treatment with cediranib, sunitinib or imatinib in comparison to U251 cells (Martinho et al., 2013). Finally, the retrieved data on drug sensitivity of NCI-60 cell line panel from CellMiner (Reinhold et al., 2012) showed that U251 and SNB19 cells differed in sensitivity to more than one third of about 110 FDA approved drugs and about 50 drugs in clinical trials. If U251, U373, and SNB19 cell lines used in mentioned works are retrospectively analyzed for authenticity and found to be isogenic, then the possible reason of the obvious individuality in drug sensitivity would be karyotype. These three cell lines diverged karyotypically, demonstrating the different chromosome modal numbers, structural and numerical complexity (Kubota et al., 2001; Roschke et al., 2003; http://www. path.cam.ac.uk/~pawefish/Links to other SKY.html). SNP array based loss of heterozygosity (LOH) and copy number variation (CNV) analysis also revealed differences between U251 and SNB19 cell lines (http:// www.sanger.ac.uk/cgi-bin/genetics/CGP/cghviewer/CghViewer.cgi). It was repeatedly documented in diverse models, including the use of isogenic cell line pairs with different chromosome instability (CIN) degree, the superior role of disturbed karyotype and CIN over gene mutations in
264
Letter to the Editor
Table 1 Summary of genetic and phenotypic/drug sensitivity characteristics of cell lines. Cell lines
U251/U373/SNB19
References
Sequencing, STR-PCR, SNP array, SKY karyotyping Different chromosome modal numbers, structural and numerical complexity
Demichelis et al. (2008), Fuxe et al. (2000), Ikediobi et al. (2006), Lorenzi et al. (2009), Timerman and Yeung (2014) Kubota et al. (2001), Roschke et al. (2003), http:// www.path.cam.ac.uk/~pawefish/Links to other SKY.html; http://www.sanger.ac.uk/cgi-bin/genetics/CGP/cghviewer/ CghViewer.cgi Fuxe et al. (2000), Ikediobi et al. (2006) Federici et al. (2013), Liu et al. (2010), Moghaddas Gholami et al. (2013), Patnaik et al. (2012) Martinho et al. (2013) Panner et al. (2005) Siegelin et al. (2009) Abaan et al. (2013), Ramis et al. (2012) See et al. (2012) Brard et al. (2009) Moghaddas Gholami et al. (2013) Martinho et al. (2013)
Studies Confirmation of cell lines similarity Evidence of karyotype divergence
Identical gene mutations Transcriptome, proteome, and phosphoproteome
CDKN2A, TP53, PTEN Differences revealed between U251 and SNB19
pRTK arrays after cediranib and sunitinib treatment Different effect on pRTKs Tested drugs/inhibitors TRAIL Comparative sensitivity U251 ≫ U373 TRAIL + quercetin U251 ≫ U373 Erlotinib U251 ≈ SNB19 N U373 MEK inhibitor U373 ≫ U251 NB7M U251 N SNB19 Paclitaxel, dasatinib U251 N SNB19 Imatinib U251 N SNB19 N U373 Sunitinib U251 N U373 N SNB19 Cediranib U251 ≈ SNB19 N U373 Temozolomide (TMZ) U251 N SNB19 TMZ + cediranib/sunitinib/imatinib U251 ≫ SNB19 ≈160 FDA approved/in clinical trials Different sensitivity of U251 Retrieved data from CellMiner (Reinhold et al., 2012) vs. SNB19 to more than one third
intrinsic and acquired cancer multidrug resistance (A'Hern et al., 2013; Duesberg et al., 2007; Lee et al., 2011; Li et al., 2005; McGranahan et al., 2012; Rasnick, 2012; Stepanenko and Kavsan, 2012). Karyotype individuality (number and structure of chromosomes and their 3D nucleus topology) determines individual genetic/signaling network (individual transcriptome/proteome) and the function and role of expressed genes (Heng et al., 2009; Stepanenko et al., 2013). Indeed, transcriptome, proteome, and phosphoproteome analysis revealed differences between U251 and SNB19 cell lines from NCI-60 cell line panel (Federici et al., 2013; Liu et al., 2010; Moghaddas Gholami et al., 2013; Patnaik et al., 2012). Some gene mutations can also contribute to differences of response to drug treatment (e.g., targeted drugs). However, from analyzed 24 cancer associated genes in U251 and SNB19 cell lines, mutations were revealed in three of them (CDKN2A, TP53, and PTEN) but all were identical among U251, U373, and SNB19 cell lines (Fuxe et al., 2000 and Refs. herein; Ikediobi et al., 2006). On the other hand, recent exome sequencing of U251 and SNB19 cells revealed some differences in global gene mutation profile (Abaan et al., 2013). Altogether, U251, U373, and SNB19 cell lines are of the same origin, show similar results in various tests but, nevertheless, represent different cell line entities with individual karyotype and drug sensitivity (Table 1). Although U251 cell line and its derivatives brought some confusion in cancer research, they can be used in elucidation of a role of cancer aneuploidy/CIN in intrinsic and acquired multidrug resistance and as a model for evolutionary dynamics of cancer genome instability. Prospectively, the whole-genome sequencing would consolidate karyotype data and shed light on the degree and complexity of the genome divergence of all three cell lines, whereas the role of karyotype individuality, heterogeneity and CIN should be emphasized in evaluation of multidrug therapy resistance in cancer research.
Conflict of Interest The authors are not aware of any affiliations, memberships, funding, or financial holdings that might be perceived as affecting the objectivity of this letter.
References Abaan, O.D., et al., 2013. The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Research 73, 4372–4382. A'Hern, R.P., et al., 2013. Taxane benefit in breast cancer — a role for grade and chromosomal stability. Nature Reviews. Clinical Oncology 10, 357–364. Brard, L., et al., 2009. Induction of cytotoxicity, apoptosis and cell cycle arrest by 1-t-butyl carbamoyl, 7-methyl-indole-3-ethyl isothiocyanate (NB7M) in nervous system cancer cells. Drug Design, Development and Therapy 2, 61–69. Demichelis, F., et al., 2008. SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Research 36, 2446–2456. Duesberg, P., et al., 2007. Cancer drug resistance: the central role of the karyotype. Drug Resistance Updates 10, 51–58. Federici, G., et al., 2013. Systems analysis of the NCI-60 cancer cell lines by alignment of protein pathway activation modules with “-OMIC” data fields and therapeutic response signatures. Molecular Cancer Research 6, 676–685. Fuxe, J., et al., 2000. Adenovirus-mediated overexpression of p15INK4B inhibits human glioma cell growth, induces replicative senescence, and inhibits telomerase activity similarly to p16INK4A. Cell Growth & Differentiation 11, 373–384. Heng, H.H., et al., 2009. Genetic and epigenetic heterogeneity in cancer: a genome-centric perspective. Journal of Cellular Physiology 220, 538–547. Ikediobi, O.N., et al., 2006. Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Molecular Cancer Therapeutics 5, 2606–2612. Kubota, H., et al., 2001. Identification of recurrent chromosomal rearrangements and the unique relationship between low-level amplification and translocation in glioblastoma. Genes, Chromosomes & Cancer 31, 125–133. Lee, A.J., et al., 2011. Chromosomal instability confers intrinsic multidrug resistance. Cancer Research 71, 1858–1870. Li, R., et al., 2005. Chromosomal alterations cause the high rates and wide ranges of drug resistance in cancer cells. Cancer Genetics and Cytogenetics 163, 44–56. Li, Y., et al., 2008. PTEN has tumor-promoting properties in the setting of gain-of-function p53 mutations. Cancer Research 2008 (68), 1723–1731. Liu, H., et al., 2010. mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities. Molecular Cancer Therapeutics 9, 1080–1091. Lorenzi, P.L., et al., 2009. DNA fingerprinting of the NCI-60 cell line panel. Molecular Cancer Therapeutics 8, 713–724. Malla, R.R., et al., 2011. Cathepsin B and uPAR knockdown inhibits tumor-induced angiogenesis by modulating VEGF expression in glioma. Cancer Gene Therapy 18, 419–434. Martinho, O., et al., 2013. In vitro and in vivo analysis of RTK inhibitor efficacy and identification of its novel targets in glioblastomas. Translational Oncology 6, 187–196. McGranahan, N., et al., 2012. Cancer chromosomal instability: therapeutic and diagnostic challenges. EMBO Reports 13, 528–538. Moghaddas Gholami, A., et al., 2013. Global proteome analysis of the NCI-60 cell line panel. Cell Reports 4, 609–620. Panner, A., et al., 2005. mTOR controls FLIPS translation and TRAIL sensitivity in glioblastoma multiforme cells. Molecular and Cellular Biology 25, 8809–8823.
Letter to the Editor Patnaik, S.K., et al., 2012. Expression of microRNAs in the NCI-60 cancer cell-lines. PLoS One 7, e49918. Ramis, G., et al., 2012. EGFR inhibition in glioma cells modulates Rho signaling to inhibit cell motility and invasion and cooperates with temozolomide to reduce cell growth. PLoS One 7, e38770. Rasnick, D., 2012. The Chromosomal Imbalance Theory of Cancer. Taylor & Francis Inc.(342 pp.). Reinhold, W.C., et al., 2012. Cell Miner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Research 72, 3499–3511. Roschke, A.V., et al., 2003. Karyotypic complexity of the NCI-60 drug-screening panel. Cancer Research 63, 8634–8647. See, W.L., et al., 2012. Sensitivity of glioblastomas to clinically available MEK inhibitors is defined by neurofibromin 1 deficiency. Cancer Research 72, 3350–3359. Siegelin, M.D., et al., 2009. Quercetin promotes degradation of survivin and thereby enhances death-receptor-mediated apoptosis in glioma cells. Neuro-Oncology 11, 122–131. Stepanenko, A.A., Kavsan, V.M., 2012. Evolutionary karyotypic theory of cancer versus conventional cancer gene mutation theory. Biopolym. Cell 28, 267–280.
265
Stepanenko, A.A., Vassetzky, Y.S., Kavsan, V.M., 2013. Antagonistic functional duality of cancer genes. Gene 529, 199–207. Timerman, D., Yeung, C.M., 2014. Identity confusion of glioma cell lines. Gene 536, 221–222. Zhao, W., et al., 2006. Fatty acid synthase: a novel target for antiglioma therapy. British Journal of Cancer 95, 869–878.
Alexey A. Stepanenko* Vadym M. Kavsan Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Kyiv 03680, Ukraine ⁎Corresponding author. E-mail address: [email protected] (A.A. Stepanenko). 6 January 2014
Contents lists available at ScienceDirect
Gene journal homepage: www.elsevier.com/locate/gene
Letter to the Editor Karyotypically distinct U251, U373, and SNB19 glioma cell lines are of the same origin but have different drug treatment sensitivities Keywords: Glioblastoma Karyotype Drug resistance Chromosome instability Aneuploidy
Dear Editor, We have read Letter to the Editor entitled Identity confusion of glioma cell lines by Timerman and Yeung (2014) and share concern and great interest to U251 and U373 cell lines misidentity and their wide use in research community as unrelated glioma cell lines. Actually, mutation analysis (Fuxe et al., 2000 and Refs. herein) and short tandem repeatspolymerase chain reaction (STR-PCR) analysis (see Refs. in Timerman and Yeung, 2014) of U373 cell stocks from The American Type Culture Collection (ATCC) and The European Collection of Cell Cultures (ECACC) revealed that U373 cells were identical to and derived from U251 cells. The picture gets more complicated with the fact that mutation analysis of cancer genes in NCI-60 cell line panel led to a suggestion that SNB19 cell line was also related to U251 cell line (Ikediobi et al., 2006). The following STR-PCR analysis of U251 and SNB19 cells showed their high similarity (Lorenzi et al., 2009) and pair-wise comparisons of the genotype calls from the single nucleotide polymorphism (SNP) mapping arrays confirmed very high identity of U251, U373, and SNB19 cell lines (Demichelis et al., 2008; http://www.sanger.ac.uk/ genetics/CGP/Genotyping/nci60.shtml). Our analysis of literature data supports the observation made by Timerman and Yeung (2014) that U251 and U373 cells behaved similarly in many works. We add that SNB19 and U251/U373 cells also demonstrated similar behavior in diverse experiments (e.g., Li et al., 2008; Malla et al., 2011; Zhao et al., 2006). However, despite the high identity and consistent results in various metrics, differences in sensitivity to drugs are well documented for this cell line lineage. It was reported that in sharp contrast to U251 cells, U373 cells (both lines of
Abbreviations: ATCC, The American Type Culture Collection; CDKN2A, cyclindependent kinase inhibitor 2A; CIN, chromosome instability; CNV, copy number variation; ECACC, The European Collection of Cell Cultures; FDA, Food and Drug Administration; FLIPS, FLICE-like inhibitory protein short; LOH, loss of heterozygosity; NCI-60, The National Cancer Institute 60 human tumor cell line anticancer drug screen; PTEN, phosphatase and tensin homolog; STR-PCR, short tandem repeats-polymerase chain reaction; SNP, single nucleotide polymorphism; S6K1, ribosomal protein S6 kinase 1; TP53, tumor protein p53; TMZ, temozolomide; TRAIL, tumor necrosis factor-related apoptosisinducing ligand.
http://dx.doi.org/10.1016/j.gene.2014.02.053 0378-1119/© 2014 Elsevier B.V. All rights reserved.
unmentioned origin) were insensitive to treatment with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). Molecular analysis revealed that cell lines differed in translation of the FLICE-like inhibitory protein short (FLIPS) mRNAs, a key regulator of TRAIL sensitivity, due to different activities of ribosomal protein S6 kinase 1 (S6K1) arm of the PI3K–mTOR–AKT pathway (Panner et al., 2005). Another research group showed that combining flavonoid quercetin with TRAIL strongly augmented TRAIL-mediated apoptosis in U251 cells but U373 cells were completely resistant (both cell lines from ATCC). The difference in sensitivity was attributed to the fact that quercetin treatment suppressed protein expression of survinin, an inhibitor of apoptosis protein, only in U251 (Siegelin et al., 2009). The growth inhibition of U251 cells was significantly more profound after erlotinib treatment (epidermal growth factor receptor inhibitor) in comparison to U373 cells (both cell lines from Institut de Recerca Hospital Universitari Vall d'Hebron, Barcelona) (Ramis et al., 2012). However, comparable erlotinib sensitivity was shown for U251 and SNB19 cells (from NCI-60 cell line panel) (Abaan et al., 2013). MEK inhibitor alone significantly reduced cell growth and cyclin D1 levels in U373 but not U251 cells (both cell lines from the UCSF BTRC Tissue Core). Only combined treatment with MEK inhibitor and dual PI3K/mTOR inhibitor induced similar response in U251 cells (See et al., 2012). SNB19 cells were more resistant to 1-t-butyl carbamoyl, 7-methyl-indole-3-ethyl isothiocyanate (NB7M), paclitaxel, and dasatinib treatment than U251 cells (both cell lines from NCI-60 cell line panel) (Brard et al., 2009; Moghaddas Gholami et al., 2013). SNB19 (from German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany) and U373 cells were less sensitive to imatinib or sunitinib treatment than U251 (the letter two lines provided by Professor Joseph Costello). Phospho-receptor tyrosine kinase (pRTK) arrays showed the different effect of cediranib and sunitinib treatment on pRTKs in U251, U373, and SNB19 cells. Furthermore, SNB19 cells were more resistant to temozolomide treatment alone or combined treatment with cediranib, sunitinib or imatinib in comparison to U251 cells (Martinho et al., 2013). Finally, the retrieved data on drug sensitivity of NCI-60 cell line panel from CellMiner (Reinhold et al., 2012) showed that U251 and SNB19 cells differed in sensitivity to more than one third of about 110 FDA approved drugs and about 50 drugs in clinical trials. If U251, U373, and SNB19 cell lines used in mentioned works are retrospectively analyzed for authenticity and found to be isogenic, then the possible reason of the obvious individuality in drug sensitivity would be karyotype. These three cell lines diverged karyotypically, demonstrating the different chromosome modal numbers, structural and numerical complexity (Kubota et al., 2001; Roschke et al., 2003; http://www. path.cam.ac.uk/~pawefish/Links to other SKY.html). SNP array based loss of heterozygosity (LOH) and copy number variation (CNV) analysis also revealed differences between U251 and SNB19 cell lines (http:// www.sanger.ac.uk/cgi-bin/genetics/CGP/cghviewer/CghViewer.cgi). It was repeatedly documented in diverse models, including the use of isogenic cell line pairs with different chromosome instability (CIN) degree, the superior role of disturbed karyotype and CIN over gene mutations in
264
Letter to the Editor
Table 1 Summary of genetic and phenotypic/drug sensitivity characteristics of cell lines. Cell lines
U251/U373/SNB19
References
Sequencing, STR-PCR, SNP array, SKY karyotyping Different chromosome modal numbers, structural and numerical complexity
Demichelis et al. (2008), Fuxe et al. (2000), Ikediobi et al. (2006), Lorenzi et al. (2009), Timerman and Yeung (2014) Kubota et al. (2001), Roschke et al. (2003), http:// www.path.cam.ac.uk/~pawefish/Links to other SKY.html; http://www.sanger.ac.uk/cgi-bin/genetics/CGP/cghviewer/ CghViewer.cgi Fuxe et al. (2000), Ikediobi et al. (2006) Federici et al. (2013), Liu et al. (2010), Moghaddas Gholami et al. (2013), Patnaik et al. (2012) Martinho et al. (2013) Panner et al. (2005) Siegelin et al. (2009) Abaan et al. (2013), Ramis et al. (2012) See et al. (2012) Brard et al. (2009) Moghaddas Gholami et al. (2013) Martinho et al. (2013)
Studies Confirmation of cell lines similarity Evidence of karyotype divergence
Identical gene mutations Transcriptome, proteome, and phosphoproteome
CDKN2A, TP53, PTEN Differences revealed between U251 and SNB19
pRTK arrays after cediranib and sunitinib treatment Different effect on pRTKs Tested drugs/inhibitors TRAIL Comparative sensitivity U251 ≫ U373 TRAIL + quercetin U251 ≫ U373 Erlotinib U251 ≈ SNB19 N U373 MEK inhibitor U373 ≫ U251 NB7M U251 N SNB19 Paclitaxel, dasatinib U251 N SNB19 Imatinib U251 N SNB19 N U373 Sunitinib U251 N U373 N SNB19 Cediranib U251 ≈ SNB19 N U373 Temozolomide (TMZ) U251 N SNB19 TMZ + cediranib/sunitinib/imatinib U251 ≫ SNB19 ≈160 FDA approved/in clinical trials Different sensitivity of U251 Retrieved data from CellMiner (Reinhold et al., 2012) vs. SNB19 to more than one third
intrinsic and acquired cancer multidrug resistance (A'Hern et al., 2013; Duesberg et al., 2007; Lee et al., 2011; Li et al., 2005; McGranahan et al., 2012; Rasnick, 2012; Stepanenko and Kavsan, 2012). Karyotype individuality (number and structure of chromosomes and their 3D nucleus topology) determines individual genetic/signaling network (individual transcriptome/proteome) and the function and role of expressed genes (Heng et al., 2009; Stepanenko et al., 2013). Indeed, transcriptome, proteome, and phosphoproteome analysis revealed differences between U251 and SNB19 cell lines from NCI-60 cell line panel (Federici et al., 2013; Liu et al., 2010; Moghaddas Gholami et al., 2013; Patnaik et al., 2012). Some gene mutations can also contribute to differences of response to drug treatment (e.g., targeted drugs). However, from analyzed 24 cancer associated genes in U251 and SNB19 cell lines, mutations were revealed in three of them (CDKN2A, TP53, and PTEN) but all were identical among U251, U373, and SNB19 cell lines (Fuxe et al., 2000 and Refs. herein; Ikediobi et al., 2006). On the other hand, recent exome sequencing of U251 and SNB19 cells revealed some differences in global gene mutation profile (Abaan et al., 2013). Altogether, U251, U373, and SNB19 cell lines are of the same origin, show similar results in various tests but, nevertheless, represent different cell line entities with individual karyotype and drug sensitivity (Table 1). Although U251 cell line and its derivatives brought some confusion in cancer research, they can be used in elucidation of a role of cancer aneuploidy/CIN in intrinsic and acquired multidrug resistance and as a model for evolutionary dynamics of cancer genome instability. Prospectively, the whole-genome sequencing would consolidate karyotype data and shed light on the degree and complexity of the genome divergence of all three cell lines, whereas the role of karyotype individuality, heterogeneity and CIN should be emphasized in evaluation of multidrug therapy resistance in cancer research.
Conflict of Interest The authors are not aware of any affiliations, memberships, funding, or financial holdings that might be perceived as affecting the objectivity of this letter.
References Abaan, O.D., et al., 2013. The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Research 73, 4372–4382. A'Hern, R.P., et al., 2013. Taxane benefit in breast cancer — a role for grade and chromosomal stability. Nature Reviews. Clinical Oncology 10, 357–364. Brard, L., et al., 2009. Induction of cytotoxicity, apoptosis and cell cycle arrest by 1-t-butyl carbamoyl, 7-methyl-indole-3-ethyl isothiocyanate (NB7M) in nervous system cancer cells. Drug Design, Development and Therapy 2, 61–69. Demichelis, F., et al., 2008. SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Research 36, 2446–2456. Duesberg, P., et al., 2007. Cancer drug resistance: the central role of the karyotype. Drug Resistance Updates 10, 51–58. Federici, G., et al., 2013. Systems analysis of the NCI-60 cancer cell lines by alignment of protein pathway activation modules with “-OMIC” data fields and therapeutic response signatures. Molecular Cancer Research 6, 676–685. Fuxe, J., et al., 2000. Adenovirus-mediated overexpression of p15INK4B inhibits human glioma cell growth, induces replicative senescence, and inhibits telomerase activity similarly to p16INK4A. Cell Growth & Differentiation 11, 373–384. Heng, H.H., et al., 2009. Genetic and epigenetic heterogeneity in cancer: a genome-centric perspective. Journal of Cellular Physiology 220, 538–547. Ikediobi, O.N., et al., 2006. Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Molecular Cancer Therapeutics 5, 2606–2612. Kubota, H., et al., 2001. Identification of recurrent chromosomal rearrangements and the unique relationship between low-level amplification and translocation in glioblastoma. Genes, Chromosomes & Cancer 31, 125–133. Lee, A.J., et al., 2011. Chromosomal instability confers intrinsic multidrug resistance. Cancer Research 71, 1858–1870. Li, R., et al., 2005. Chromosomal alterations cause the high rates and wide ranges of drug resistance in cancer cells. Cancer Genetics and Cytogenetics 163, 44–56. Li, Y., et al., 2008. PTEN has tumor-promoting properties in the setting of gain-of-function p53 mutations. Cancer Research 2008 (68), 1723–1731. Liu, H., et al., 2010. mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities. Molecular Cancer Therapeutics 9, 1080–1091. Lorenzi, P.L., et al., 2009. DNA fingerprinting of the NCI-60 cell line panel. Molecular Cancer Therapeutics 8, 713–724. Malla, R.R., et al., 2011. Cathepsin B and uPAR knockdown inhibits tumor-induced angiogenesis by modulating VEGF expression in glioma. Cancer Gene Therapy 18, 419–434. Martinho, O., et al., 2013. In vitro and in vivo analysis of RTK inhibitor efficacy and identification of its novel targets in glioblastomas. Translational Oncology 6, 187–196. McGranahan, N., et al., 2012. Cancer chromosomal instability: therapeutic and diagnostic challenges. EMBO Reports 13, 528–538. Moghaddas Gholami, A., et al., 2013. Global proteome analysis of the NCI-60 cell line panel. Cell Reports 4, 609–620. Panner, A., et al., 2005. mTOR controls FLIPS translation and TRAIL sensitivity in glioblastoma multiforme cells. Molecular and Cellular Biology 25, 8809–8823.
Letter to the Editor Patnaik, S.K., et al., 2012. Expression of microRNAs in the NCI-60 cancer cell-lines. PLoS One 7, e49918. Ramis, G., et al., 2012. EGFR inhibition in glioma cells modulates Rho signaling to inhibit cell motility and invasion and cooperates with temozolomide to reduce cell growth. PLoS One 7, e38770. Rasnick, D., 2012. The Chromosomal Imbalance Theory of Cancer. Taylor & Francis Inc.(342 pp.). Reinhold, W.C., et al., 2012. Cell Miner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Research 72, 3499–3511. Roschke, A.V., et al., 2003. Karyotypic complexity of the NCI-60 drug-screening panel. Cancer Research 63, 8634–8647. See, W.L., et al., 2012. Sensitivity of glioblastomas to clinically available MEK inhibitors is defined by neurofibromin 1 deficiency. Cancer Research 72, 3350–3359. Siegelin, M.D., et al., 2009. Quercetin promotes degradation of survivin and thereby enhances death-receptor-mediated apoptosis in glioma cells. Neuro-Oncology 11, 122–131. Stepanenko, A.A., Kavsan, V.M., 2012. Evolutionary karyotypic theory of cancer versus conventional cancer gene mutation theory. Biopolym. Cell 28, 267–280.
265
Stepanenko, A.A., Vassetzky, Y.S., Kavsan, V.M., 2013. Antagonistic functional duality of cancer genes. Gene 529, 199–207. Timerman, D., Yeung, C.M., 2014. Identity confusion of glioma cell lines. Gene 536, 221–222. Zhao, W., et al., 2006. Fatty acid synthase: a novel target for antiglioma therapy. British Journal of Cancer 95, 869–878.
Alexey A. Stepanenko* Vadym M. Kavsan Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Kyiv 03680, Ukraine ⁎Corresponding author. E-mail address: [email protected] (A.A. Stepanenko). 6 January 2014